/**
 * \file  distance_matrix.h
 * \brief Definition of Distance Matrix.
 *
 * LAV: Lib Anti Virals
 * <http://lav.googlecode.com/>
 * Copyright (C) 2010 Velez Ezequiel, Peralta Andres, FuDePAN
 *
 * This file is part of the LAV project.
 *
 * Contents:       Header file for LAV providing Distance Matrix.
 *
 * System:         LAV
 * Language:       C++
 *
 * Author:         Velez Ezequiel, Peralta Andres
 * E-Mail:
 *
 * LAV is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * LAV is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with LAV.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifndef DISTANCE_MATRIX_H
#define DISTANCE_MATRIX_H

#include "lav/sequence.h"


namespace lav
{

// Define the size of matrix (4 = A U C G)
const size_t SIZE_MATRIX = 4;    

// Global variable DistanceMatrix
extern biopp::DistanceMatrix _matrix;    


/**
 * This method defines the matrix of distances between nucleotids
 *
 *@Param defaultm Represents the information loaded in the matrix.
 *
 */
void set_default_matrix(biopp::DistanceMatrix& defaultm);

}

#endif

